The genotypes or phenotypes of geographically representative samples of rhesus macaques, Macaca mulatta, of different subspecies of Chinese, Indian and southeast Asian origin will be compared in phylogenetic context (i.e., together with those of six other species of macaques) using approximately 75 DNA loci, amplified using the polymerase chain recation (PCR), to genetically characterize these taxa These genetic differences will be compared among various hierarchical levels (e.g. regional populations, subspecies, countries of origin, species) of macaques to assess their biological significance using gene diversity and phylogenetic methods and each taxa will be genetically characterized with specific marker alleles relative to each other. The loci to be studied include neutral (STR) loci widely dispersed over all chromosomes, mt DNA, a Y-chromosome haplotype,and both class I and class II MHC loci which influence immune responsiveness. A program to assign samples of unknown provenience to their correct subspecies, geographic region or country of origin, now in use, will be substantially improved using the new population samples and genetic data generated by this grant. Services provided to all nonhuman primate breeding facilities by this grant include typing rhesus macaques using 15 most informative STR loci to establish pedigrees, the use of these data to estimate genetic parameters such as effective population size, inbreeding and average kinship coefficients, gene diversity, generate a genetic profile of individual animals, conduct paternity exclusion analysis for estimating relative reproductive success of male breeders and specific founding lineages and the use of the aforementioned assignment program and taxa-specific genetic markers identified during the course of this study to identify the country of origin and subspecies of samples of unknown origin. In addition, specific recommendations tailored to the unique facilities at each SPF breeding colony supported by NIH will be prepared and provided to each colony to facilitate maintenance of genetic heterogeneity. PERFORMANCE SIT_t_j (orgam2atlon, c/,_(, state) Department of Anthropology, Veterinary Genetics Laboratory (VGL) and California Regional Primate Research Center (CRPRC) University of California One Shields Avenue Davis,CA 95616 KEY PERSONNEL. See instructions. Start with Principal Investigator. List all Name David Glenn Smith John Ely Sreetharan Kanthaswamy Donald J.Melnick Cecilia Penedo Jeffrey Roberts Charles Southwick Use continuation pages as needed the required other key personnel in alphabetical order, last name first. Organization Role on Project Department of Anthropology & CRPRC P.i. Lab.Mol. EvoI.Genom., Bioqual, Inc. Consultant CRPRC (50%) and VGL (50%) Collaborator Columbia University Collaborator VGL,UC Davis Collaborator CRPRC Collaborator University of Colorado Consultant to provide information in the format shown below. Disclosure Permission Statement. Applicable to SBIR/STTR Only. See instructions, [] Yes [] No Principal Investigator/Program Director (Last, first, middle): SMITH, David G] enn Role of all Personnel and Staff on Project Dr. David Glenn Smith, an anthropologist with a strong background in genetics, w_li provide die major direction, assume responsibility and serve as P.I. for this grant. He will receixe 2/9 of his salary from this grant to release him from teaching duties during the winter quarter of each year and will cvx)rdinate among the projects conducted at the other U.C. and outside laboratories that pertain to the specific aims of this grant. Unnamed: a Staff Research Associate III will be hired to replace Dr. Sreetharan Kanthaswamy who will assume a new position, efli_ctive 01/01/03 at the VGL and CRPRC. He/she will receive 100% c)f his/her salar> from this grant and will supervise all procedures to be conducted at laboratories in the Anthropology Department and serve as liaison to other U.C and outside laboratories collaborating on this project. He/she will take direct responsibility for supervising the analysis of STR loci by the PGR Ill, described below, and the restriction analysis of MtDNA and MHC PCR fragments by thePGR iV, described below, of the 1250 samples to be studied, and will assign genotypes to all loci and haplotypes to MHC, Y-chromosome and mtDNA and record all data in an EXCEL file, He/she will work closely with Dr. Kanthaswamy in the population genetic and phylogenetic analyses of data. He will receive 100% of his salary from this grant. Cam Monroe, a PGR III, will work under the supervision of the (unnamed) SRA III described, above, and will draw 100% of her salary from this grant, on which she for the last year. She will be directly responsible for extracting and inventorying all DNA employed in this study and conducting routine PCR amplification of 59 STR loci (including Y-linked STR loci) under supervision of the SRA III, described above, and will assist the PGR IV, described below, in the restriction analysis of MHC loci and mtDNA to construct haplotypes. Site will assist the SRA IIi in maintaining a centralized lile of all data generated by this grant and developing a genetic data reference panel for the subspecies and region and country' of origin assignment program. She will assume the major responsibility for testing samples of unknown provenience to assigned them to a region of origin using the assignment program. Unnamed: This position will be tilled by a PGR tV and will receive 50% of his/her salary from this grant. His/her major responsibility will be the amplification and restriction analysis of MtDNA and MHC loci, at which tasks she will be assisted by the PGR III described above and supervised by the SPA III, described above. Dr. Sreetharan Kanthaswamy, Assistant research Geneticist, recently received his Ph.D. degree in genetics and, effecuve 01/01/03, will assume duties of 50% appointments at the VGL and CRPRC. Prior to this appointment, her served as lab manager to the present P.I. and was actively involved in the research described in section C (l_'ogmss report) of this grant application. His former position is that to be assumed by the SRA III, described alx-_ve. Dr. Kanthaswam 3 will collaborale with us on the sequencing and restriction analysis of mtDNA and characterization of the Mama-A*01 phenotype. He will participate in the construction of mtDNA haplotypes during thcr first three years of this grant, superxise the population genetic and phylogenetic analyses to occur during years 4 and 5 and help in the prepmation of genetic management reports to SPF breeding colonies being supported by Nil t. I[e will receive 10% of his sala U from this grant. Dr. Cecilia Peneda has a Ph.D. in Genetics and is a Staff Research Associate at the Veterina U Genetics Laborators. She will receive 10% salary support from this grant. Her duties will include directing the analyses of 15 STR loci to be analyzed for up to 500 SPF rhesus macaques whose breeding is supported by NIH. She will maintain a data base containing STR genotypes of these monkeys to be used to estimate genetic parameters used li_)rmaking genetic management recommendations to these breeding colonies.. Dr. Jeffrey Roberts, assistant director for primate medicine at the California Regional Primate Research Center (CRPRC) will serve as a collaborator on this grant but _ill receive no salary from the grant. He is currentl} P.i. on a grant from the NCRR to breed SPF rhesus macaqt|es and has provided portions of the samples to be studied as a part of the present grant and facilitated our acquisition of others of these samples from other primate breeding facilities. In addition to continuing to serve the present grant in this capacity, Dr. Roberts will facilitate the transfer of knowledge and methodology developed as a part of the present grant to genetic analyses employed by the VGL to type SPF rhesus macaques for genetic management purposes. DblR "),ClR/gAClpound1 (l:?au rlR/_-I "_ D_n_ _ t't.nn'l'in.=l'i,,_n l:nn"n='l" P=na Pnncipal InvestJgatodProgram Director (Last, first, middle): SNITH, Day id G] enn Dr. Donald J. Melnick, a collaborator on this grant, will advice us on the selection of PCR primers lor amplifying mitochondrial and Y-chromosome DNA fragments in the macaque samples to be studied and on the gene diversity and phylogenetic analyses to be conducted as part of this grant, both areas in which Dr. Melnick andf his staff are very experienced and extensively published. In addition, Dr. Melnick provided DNA samples fi'om the Dunga Gall population of rhesus macaques from Pakistan, which represent the westernmost representatives of Macaca mulatta to be studied and, as such, are a crucial population for this study. Dr. Charles Southwick will serve this grant as an unpaid consultant on the biogeography of rhesus macaques, a subject on which he is widely recognized as a leading world authority. He provided significant invaluable information and advice pertaining to the representative sampling of rhesus macaque populations and subspecies and macaque species to be studied as part of this grant and will continue to serve in this role during the course of this grant as other samples become available on an opportunistic basis. Dr. John Ely will serve as a paid consultant on this grant. Dr. Ely has been instrumental in helping my lab to install PEDSYS and other genetic management software and will continue to serve in this role during the tenure of this grant. In addition, Dr. Ely has, and will continue to, advise us in our selection of STR loci to employ for this study. It is likely that additional, more informative STR loci will be identified by us or others during the course of this grant and we will replace other less informative STR loci with these, following Dr. Ely's advice. [_MN _Q_/_QI'I (l_l fl_/fl9 _ D_t_ 4 _.t_ofinH_tlan Igrlrrn_f P_n_ Principal InvestigatodProgram Director (Last, first, middle): The name of the principal investigator/program director must be provided at the top of each printed page and each continuation page. RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page ................................................................................................................................................ 1 Description,